Quantitative measurement of pathogen specific human memory T cell repertoire diversity using a CDR3β-specific microarray

详细信息    查看全文

• 作者：Xujing Wang (1) (2)
  Shuang Jia (1)
  Lisa Meyer (1)
  Maryam B Yassai (3)
  Yuri N Naumov (4)
  Jack Gorski (3)
  Martin J Hessner (1) (2)
  
• 刊名：BMC Genomics
• 出版年：2007
• 出版时间：December 2007
• 年：2007
• 卷：8
• 期：1
• 全文大小：436KB
• 参考文献：1. Davis MM, Bjorkman PJ: T-cell antigen receptor genes and T-cell recognition. / Nature 1988, 334:395-02. CrossRef
  2. Turner SJ, Doherty PC, McCluskey J, Rossjohn J: Structural determinants of T-cell receptor bias in immunity. / Nat Rev Immunol 2006, 6:883-94. CrossRef
  3. Lehner PJ, Wang EC, Moss PA, Williams S, Platt K, Friedman SM, Bell JI, Borysiewicz LK: Human HLA-A0201-restricted cytotoxic T lymphocyte recognition of influenza A is dominated by T cells bearing the V beta 17 gene segment. / J Exp Med 1995, 181:79-1. jem.181.1.79">CrossRef
  4. Moss DJ, Burrows SR, Baxter GD, Lavin MF: T cell-T cell killing is induced by specific epitopes: evidence for an apoptotic mechanism. / J Exp Med 1991, 173:681-86. jem.173.3.681">CrossRef
  5. Arstila TP, Casrouge A, Baron V, Even J, Kanellopoulos J, Kourilsky P: A direct estimate of the human alphabeta T cell receptor diversity. / Science 1999, 286:958-61. CrossRef
  6. Arstila TP, Casrouge A, Baron V, Even J, Kanellopoulos J, Kourilsky P: Diversity of human alpha beta T cell receptors. / Science 2000, 288:1135. CrossRef
  7. Maslanka K, Piatek T, Gorski J, Yassai M: Molecular analysis of T cell repertoires. Spectratypes generated by multiplex polymerase chain reaction and evaluated by radioactivity or fluorescence. / Hum Immunol 1995, 44:28-4. CrossRef
  8. Naumov YN, Hogan KT, Naumova EN, Pagel JT, Gorski J: A class I MHC-restricted recall response to a viral peptide is highly polyclonal despite stringent CDR3 selection: implications for establishing memory T cell repertoires in "real-world" conditions. / J Immunol 1998, 160:2842-852.
  9. Gorski J, Yassai M, Zhu X, Kissela B, Kissella B, Keever C, Flomenberg N: Circulating T cell repertoire complexity in normal individuals and bone marrow recipients analyzed by CDR3 size spectratyping. Correlation with immune status. / J Immunol 1994, 152:5109-119.
  10. Gorski J, Piatek T, Yassai M, Maslanka K: Improvements in repertoire analysis by CDR3 size spectratyping. Bifamily PCR. / Ann N Y Acad Sci 1995, 756:99-02. j.1749-6632.1995.tb44490.x">CrossRef
  11. Douek DC, Betts MR, Brenchley JM, Hill BJ, Ambrozak DR, Ngai KL, Karandikar NJ, Casazza JP, Koup RA: A novel approach to the analysis of specificity, clonality, and frequency of HIV-specific T cell responses reveals a potential mechanism for control of viral escape. / J Immunol 2002, 168:3099-104.
  12. Naumov YN, Naumova EN, Gorski J: CD4+ and CD8+ circulating alpha/beta T-cell repertoires are equally complex and are characterized by different levels of steady-state TCR expression. / Hum Immunol 1996, 48:52-2. CrossRef
  13. Naumov YN, Naumova EN, Clute SC, Watkin LB, Kota K, Gorski J, Selin LK: Complex T cell memory repertoires participate in recall responses at extremes of antigenic load. / J Immunol 2006, 177:2006-014.
  14. Naumov YN, Naumova EN, Hogan KT, Selin LK, Gorski J: A fractal clonotype distribution in the CD8+ memory T cell repertoire could optimize potential for immune responses. / J Immunol 2003, 170:3994-001.
  15. Hessner MJ, Singh VK, Wang X, Khan S, Tschannen MR, Zahrt TC: Utilization of a labeled tracking oligonucleotide for visualization and quality control of spotted 70-mer arrays. / BMC Genomics 2004, 5:12. CrossRef
  16. Hessner MJ, Baxter-Lowe LA: Characterization of novel HLA-DPB1 alleles by oligotyping and nucleotide sequencing. / Tissue Antigens 1992, 40:261-63. j.1399-0039.1992.tb02055.x">CrossRef
  17. Baxter-Lowe LA, Hunter JB, Casper JT, Gorski J: HLA gene amplification and hybridization analysis of polymorphism. HLA matching for bone marrow transplantation of a patient with HLA-deficient severe combined immunodeficiency syndrome. / J Clin Invest 1989, 84:613-18. CrossRef
  18. Storey JD: A direct approach to false discovery rates. / Journal of the Royal Statistical Society 2002, 64:479-98.
  19. Shi L, Tong W, Goodsaid F, Frueh FW, Fang H, Han T, Fuscoe JC, Casciano DA: QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. / Expert Rev Mol Diagn 2004, 4:761-77. CrossRef
  20. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W: Multiple-laboratory comparison of microarray platforms. / Nat Methods 2005, 2:345-50. CrossRef
  21. Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J: Independence and reproducibility across microarray platforms. / Nat Methods 2005, 2:337-44. CrossRef
  22. Shi L, Tong W, Fang H, Scherf U, Han J, Puri RK, Frueh FW, Goodsaid FM, Guo L, Su Z, Han T, Fuscoe JC, Xu ZA, Patterson TA, Hong H, Xie Q, Perkins RG, Chen JJ, Casciano DA: Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. / BMC Bioinformatics 2005, 6 Suppl 2:S12. CrossRef
  23. Hessner MJ, Meyer L, Tackes J, Muheisen S, Wang X: Immobilized probe and glass surface chemistry as variables in microarray fabrication. / BMC Genomics 2004, 5:53. CrossRef
  24. Hessner MJ, Wang X, Khan S, Meyer L, Schlicht M, Tackes J, Datta MW, Jacob HJ, Ghosh S: Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility. / Nucleic Acids Res 2003, 31:e60. CrossRef
  25. Chou CC, Chen CH, Lee TT, Peck K: Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. / Nucleic Acids Res 2004, 32:e99. CrossRef
  26. Relogio A, Schwager C, Richter A, Ansorge W, Valcarcel J: Optimization of oligonucleotide-based DNA microarrays. / Nucleic Acids Res 2002, 30:e51. CrossRef
  27. Guo Z, Guilfoyle RA, Thiel AJ, Wang R, Smith LM: Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. / Nucleic Acids Res 1994, 22:5456-465. CrossRef
  28. Ogle BM, Cascalho M, Joao C, Taylor W, West LJ, Platt JL: Direct measurement of lymphocyte receptor diversity. / Nucleic Acids Res 2003, 31:e139. CrossRef
  29. Bonarius HP, Baas F, Remmerswaal EB, van Lier RA, Berge IJ, Tak PP, de Vries N: Monitoring the T-cell receptor repertoire at single-clone resolution. / PLoS ONE 2006, 1:e55. journal.pone.0000055">CrossRef
  30. Diehl F, Grahlmann S, Beier M, Hoheisel JD: Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. / Nucleic Acids Research 2001, 29:e38. CrossRef
  31. Yassai M, Naumova E, Gorski J: Generation of TCR spectratypes by multiplex PCR for T cell repertoire analysis. / (Edited by: Oksenberg JR). Austin, TX, Landes Bioscience 1997, The Antigen T Cell Receptor: Selected Protocols and Applications. Austin, TX: Landes Bioscience;:326-72.
  32. Wang X, Ghosh S, Guo SW: Quantitative quality control in microarray image processing and data acquisition. / Nucleic Acids Research 2001, 29:E75-2. CrossRef
  33. Wang X, Jiang N, Feng X, Xie Y, Tonellato PJ, Ghosh S, Hessner MJ: A novel approach for high-quality microarray processing using third-dye array visualization technology. / IEEE Trans Nanobioscience 2003, 2:193-01. CrossRef
  
• 作者单位：Xujing Wang (1) (2)
  Shuang Jia (1)
  Lisa Meyer (1)
  Maryam B Yassai (3)
  Yuri N Naumov (4)
  Jack Gorski (3)
  Martin J Hessner (1) (2)
  
  1. The Max McGee National Research Center for Juvenile Diabetes, Department of Pediatrics, The Medical College of Wisconsin and The Children's Hospital Research Institute of Children's Hospital of Wisconsin, Watertown Plank Road, 8701, Milwaukee, WI, 53226, USA
  2. The Human and Molecular Genetics Center, The Medical College of Wisconsin, Watertown Plank Road, 8701, Milwaukee, WI, 53226, USA
  3. Department of Pathology, University of Massachusetts Medical School, Lake Avenue North, 55, Worcester, MA, 01655, USA
  4. The Blood Research Institute, BloodCenter of Wisconsin, Watertown Plank Road, 8727, Milwaukee, Wisconsin, 53226, USA
  

文摘

Background Providing quantitative microarray data that is sensitive to very small differences in target sequence would be a useful tool in any number of venues where a sample can consist of a multiple related sequences present in various abundances. Examples of such applications would include measurement of pseudo species in viral infections and the measurement of species of antibodies or T cell receptors that constitute immune repertoires. Difficulties that must be overcome in such a method would be to account for cross-hybridization and for differences in hybridization efficiencies between the arrayed probes and their corresponding targets. We have used the memory T cell repertoire to an influenza-derived peptide as a test case for developing such a method. Results The arrayed probes were corresponded to a 17 nucleotide TCR-specific region that distinguished sequences differing by as little as a single nucleotide. Hybridization efficiency between highly related Cy5-labeled subject sequences was normalized by including an equimolar mixture of Cy3-labeled synthetic targets representing all 108 arrayed probes. The same synthetic targets were used to measure the degree of cross hybridization between probes. Reconstitution studies found the system sensitive to input ratios as low as 0.5% and accurate in measuring known input percentages (R2 = 0.81, R = 0.90, p < 0.0001). A data handling protocol was developed to incorporate the differences in hybridization efficiency. To validate the array in T cell repertoire analysis, it was used to analyze human recall responses to influenza in three human subjects and compared to traditional cloning and sequencing. When evaluating the rank order of clonotype abundance determined by each method, the approaches were not found significantly different (Wilcoxon rank-sum test, p > 0.05). Conclusion This novel strategy appears to be robust and can be adapted to any situation where complex mixtures of highly similar sequences need to be quantitatively resolved.